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vg 1.48.0 - Gallipoli
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@jeizenga jeizenga released this 08 May 22:43
· 543 commits to master since this release
v1.48.0
f478c7f
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Learn about vigilant mode.

Download for Linux

Don't forget to mark the static binary executable:

chmod +x vg

Docker Image: quay.io/vgteam/vg:v1.48.0

Buildable Source Tarball: vg-v1.48.0.tar.gz

Includes source for vg and all submodules. Use this instead of Github's "Source Code" downloads; those will not build as they do not include code for bundled dependencies that the vg build process needs.

This release includes:

  • vg chunk will now report an error if asked to chunk reads that do not go with the graph
  • vg autoindex can construct linear reference indexes from a FASTA file
  • vg gbwt will now refuse to add reference sample names with # in them, and will try and advise on what the tags are supposed to be like
  • vg surject can project to paths that intersect themselves in the reverse orientation
  • vg surject will now print warning messages when processing a read or pair takes a suspiciously long amount of time.
  • vg giraffe should no longer try to put hypothetical sequencing errors in empty intervals, and should report errors in MAPQ cap computation in a more debuggable way.
  • Crashes now include the stack trace by default; set VG_FULL_TRACEBACK=0 to suppress it to a file.
  • vg surject and vg giraffe should now include relevant read name hints when crashing in many cases.
  • Added crash_unless() as an alternative to assert() that reports these hints. We eventually want to use it everywhere.
  • Crash reports now have cool hyperlinks.
  • vg surject will limit itself to 200 anchors per target path segment by default; use the new -a/--max-anchors option to control this limit. Surjection against PGGB graphs may require --max-anchors 20 to complete.
  • vg surject may be able to limit itself to considering only high-scoring surjections in some cases.
  • vg construct now properly handles the case where it is looking for the end of an inversion from 1 base before it
  • vg construct will no longer try and coalesce nodes at construction chunk boundaries when those nodes have alt paths that visit them or edges to their outside endpoints. This should fix some crashes and incorrect placement of structural variant breakpoints in the graph.
  • Update vcflib to current version plus build and parser fixes
  • vg construct should now be faster when variants are extremely long and overlap each other
  • vg chunk now outputs PackedGraph instead of Protobuf by default (unless -T is used). Also, output files now get the .vg file extension for any non-GFA format (use vg stats -F to check the underlying format of any graph).
  • Snarl clipping bug in vg clip fixed so that when there are multiple different reference traversals in a snarl (common in PGGB output), then none of them are chopped.
  • Fixed build against Ubuntu 22.04's pybind11
  • Docker containers now have /usr/bin/time for profiling

Updated Submodules

  • htslib
  • vcflib
  • gbwtgraph
  • libbdsg
  • tabixpp
Assets 4
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